GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mglC in Pseudomonas fluorescens FW300-N1B4

Align Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate Pf1N1B4_6033 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)

Query= TCDB::G4FGN4
         (313 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6033 Ribose ABC transport
           system, permease protein RbsC (TC 3.A.1.2.1)
          Length = 325

 Score =  173 bits (438), Expect = 6e-48
 Identities = 107/304 (35%), Positives = 163/304 (53%), Gaps = 3/304 (0%)

Query: 12  GIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSIL 71
           G+   L+A+V    V +  FL+ +   T+   +  + +++ GMT V+I  GIDLSVGS+L
Sbjct: 22  GLAGALLAMVALFSVLSSHFLSYDTFSTLANQIPDLMVLAVGMTFVLIIGGIDLSVGSVL 81

Query: 72  GAASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRG 131
             A+  + + +   G S   + ++G+AV    G   G +    R+  FI +LG+L + RG
Sbjct: 82  ALAASAVSVAILGWGWSVLPAALLGMAVAALAGTITGSITVAWRIPSFIVSLGVLEMARG 141

Query: 132 LAYVMSGGWPISPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTGRRIYAIG 191
           LAY M+G    +   ++F      +   +    I   +I  IA   L  TV GR +  IG
Sbjct: 142 LAYQMTGS-RTAYIGDAFAWLSNPIAFGISPSFIIALLIIFIAQAVLTRTVFGRYLIGIG 200

Query: 192 GNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVIAATVI 251
            N EA +L GI      ILV+++ G LA  A     + L  A PNAG G EL VIAA VI
Sbjct: 201 TNEEAVRLAGINPKPYKILVFSLMGLLAGIAALFQISRLEAADPNAGSGLELQVIAAVVI 260

Query: 252 GGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAIDQIR--R 309
           GGTSL GG G+++  F G +I+ VL  G+  +G +   ++++ G VI++A+ +D  R  R
Sbjct: 261 GGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTKRIITGAVIVVAVVLDTYRSQR 320

Query: 310 AKER 313
           A  R
Sbjct: 321 ASRR 324


Lambda     K      H
   0.328    0.145    0.421 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 279
Number of extensions: 9
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 313
Length of database: 325
Length adjustment: 28
Effective length of query: 285
Effective length of database: 297
Effective search space:    84645
Effective search space used:    84645
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory